compbio.runner
Class _SkeletalCommandBuilder

java.lang.Object
  compbio.runner._SkeletalCommandBuilder

All Implemented Interfaces:

Executable<_SkeletalCommandBuilder>

Direct Known Subclasses:

BlastAll, Disembl, Mcl, OB, PSIBlast, Ronn, RPSBlast

public abstract class _SkeletalCommandBuilder
extends java.lang.Object
implements Executable<_SkeletalCommandBuilder>

Nested Class Summary

Nested classes/interfaces inherited from interface compbio.engine.client.Executable

Executable.ExecProvider

Constructor Summary

_SkeletalCommandBuilder()

Method Summary

_SkeletalCommandBuilder	addParameter(java.lang.String parameter)
_SkeletalCommandBuilder	addParameters(java.util.List<java.lang.String> parameters) Adds parameter to the list of parameters for a native executable
_SkeletalCommandBuilder	addParameters(java.lang.String[] parameters)
java.lang.String	getEmail()
java.lang.String	getError()
Limit<_SkeletalCommandBuilder>	getLimit(java.lang.String presetName)
LimitsManager<_SkeletalCommandBuilder>	getLimits()
java.lang.String	getName()
java.lang.String	getOutput()
CommandBuilder<_SkeletalCommandBuilder>	getParameters(Executable.ExecProvider provider)
<V> V	getResults(java.lang.String directory)
Executable<?>	loadRunConfiguration(RunConfiguration rconfig)
_SkeletalCommandBuilder	setEmail(java.lang.String email)
_SkeletalCommandBuilder	setName(java.lang.String name)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface compbio.engine.client.Executable

getCreatedFiles, getInput

Constructor Detail

_SkeletalCommandBuilder

public _SkeletalCommandBuilder()

Method Detail

setEmail

public _SkeletalCommandBuilder setEmail(java.lang.String email)

setName

public _SkeletalCommandBuilder setName(java.lang.String name)

getName

public java.lang.String getName()

getEmail

public java.lang.String getEmail()

addParameters

public _SkeletalCommandBuilder addParameters(java.lang.String[] parameters)

addParameters

public _SkeletalCommandBuilder addParameters(java.util.List<java.lang.String> parameters)

Description copied from interface: Executable

Adds parameter to the list of parameters for a native executable

Specified by:

addParameters in interface Executable<_SkeletalCommandBuilder>

Returns:

this Executable

getParameters

public CommandBuilder<_SkeletalCommandBuilder> getParameters(Executable.ExecProvider provider)

Specified by:

getParameters in interface Executable<_SkeletalCommandBuilder>

addParameter

public _SkeletalCommandBuilder addParameter(java.lang.String parameter)

getResults

public <V> V getResults(java.lang.String directory)

Specified by:

getResults in interface Executable<_SkeletalCommandBuilder>

loadRunConfiguration

public Executable<?> loadRunConfiguration(RunConfiguration rconfig)

Specified by:

loadRunConfiguration in interface Executable<_SkeletalCommandBuilder>

getOutput

public java.lang.String getOutput()

Specified by:

getOutput in interface Executable<_SkeletalCommandBuilder>

getError

public java.lang.String getError()

Specified by:

getError in interface Executable<_SkeletalCommandBuilder>

getLimit

public Limit<_SkeletalCommandBuilder> getLimit(java.lang.String presetName)

Specified by:

getLimit in interface Executable<_SkeletalCommandBuilder>

getLimits

public LimitsManager<_SkeletalCommandBuilder> getLimits()

Specified by:

getLimits in interface Executable<_SkeletalCommandBuilder>